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- PDB-6mfk: Crystal Structure of Chloramphenicol Acetyltransferase from Eliza... -

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Basic information

Entry
Database: PDB / ID: 6mfk
TitleCrystal Structure of Chloramphenicol Acetyltransferase from Elizabethkingia anophelis
ComponentsChloramphenicol acetyltransferase
KeywordsTRANSFERASE / SSGCID / antibiotic resistance / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase activity / chloramphenicol O-acetyltransferase / response to antibiotic
Similarity search - Function
: / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesElizabethkingia anophelis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2021
Title: Structural characterization of a Type B chloramphenicol acetyltransferase from the emerging pathogen Elizabethkingia anophelis NUHP1.
Authors: Ghafoori, S.M. / Robles, A.M. / Arada, A.M. / Shirmast, P. / Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Myler, P.J. / Edwards, T.E. / Kuhn, M.L. / Forwood, J.K.
History
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9746
Polymers24,4761
Non-polymers4985
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chloramphenicol acetyltransferase
hetero molecules

A: Chloramphenicol acetyltransferase
hetero molecules

A: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,92218
Polymers73,4283
Non-polymers1,49415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14720 Å2
ΔGint-202 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.950, 102.950, 115.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-302-

PO4

21A-302-

PO4

31A-517-

HOH

41A-567-

HOH

51A-600-

HOH

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Components

#1: Protein Chloramphenicol acetyltransferase / Type B chloramphenicol O-acetyltransferase


Mass: 24475.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis (bacteria) / Gene: catB, BAY10_06425, E18064_290343 / Plasmid: ElanA.01572.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: X5KVH4, chloramphenicol O-acetyltransferase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ElanA.01572.a.B1.PW38419 @21.17 mg/ml was incubated with 5 mM acetyl-CoA and chloramphenicol, then mixed 1:1 with JCSG+(a11): 50% (v/v) MPD, 0.1 M Tris base/ HCl, pH = 8.5, 0.2 M ammonium ...Details: ElanA.01572.a.B1.PW38419 @21.17 mg/ml was incubated with 5 mM acetyl-CoA and chloramphenicol, then mixed 1:1 with JCSG+(a11): 50% (v/v) MPD, 0.1 M Tris base/ HCl, pH = 8.5, 0.2 M ammonium phosphate basic. Tray 299552a11, puck: jtk9-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 19, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→38.423 Å / Num. obs: 28379 / % possible obs: 99.9 % / Redundancy: 7.882 % / Biso Wilson estimate: 31.595 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.051 / Χ2: 1.041 / Net I/σ(I): 21.49 / Num. measured all: 223684
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.698.1190.5183.916750206320630.9340.553100
1.69-1.748.1110.4065.0516424202520250.9580.434100
1.74-1.798.1420.3036.6816000196519650.9750.324100
1.79-1.848.0910.2368.415608192919290.9840.253100
1.84-1.918.0680.17511.3515079186918690.9880.188100
1.91-1.978.0630.14113.6814514180018000.9930.151100
1.97-2.057.9730.1117.0913737172417230.9950.11899.9
2.05-2.137.9050.08920.8313304168316830.9950.096100
2.13-2.227.8820.07424.0412690161016100.9960.08100
2.22-2.337.7660.06826.3411889153115310.9960.073100
2.33-2.467.7860.06128.2611461147514720.9970.06699.8
2.46-2.617.7460.05730.6210751138813880.9970.061100
2.61-2.797.7170.05133.9310125131313120.9980.05599.9
2.79-3.017.6290.04636.659269121712150.9980.0599.8
3.01-3.37.540.04339.248513113411290.9980.04799.6
3.3-3.697.4720.03841.137607102010180.9990.0499.8
3.69-4.267.580.03542.8468759099070.9990.03899.8
4.26-5.227.6480.0343.4659127767730.9990.03299.6
5.22-7.387.6830.03143.147256176150.9990.03499.7
7.38-38.4236.9630.03441.424513593520.9980.03898.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.14_3228)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XAT

1xat


Resolution: 1.65→38.423 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.81
RfactorNum. reflection% reflection
Rfree0.1635 1670 6.03 %
Rwork0.1453 --
obs0.1464 27679 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.13 Å2 / Biso mean: 29.7393 Å2 / Biso min: 12.49 Å2
Refinement stepCycle: final / Resolution: 1.65→38.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 28 209 1886
Biso mean--80.08 38.99 -
Num. residues----210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6499-1.69850.21081400.19162005214592
1.6985-1.75330.22661230.17382048217193
1.7533-1.8160.16181350.17022105224095
1.816-1.88870.18711310.1532116224796
1.8887-1.97460.20471460.1592170231698
1.9746-2.07870.19171110.15352188229998
2.0787-2.2090.16831530.14072191234499
2.209-2.37950.16561280.14582209233799
2.3795-2.61890.18961520.15542221237399
2.6189-2.99770.17351610.150421882349100
2.9977-3.77630.17151340.134522542388100
3.7763-38.43370.12351560.13523142470100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.57780.0815-0.14552.90620.32491.50280.0137-0.50830.12050.3318-0.0494-0.1942-0.06720.0420.06170.22020.0028-0.05730.2198-0.02890.12747.314513.68134.3137
23.0069-1.83790.05191.5314-0.10010.0617-0.0743-0.08710.17210.05250.0424-0.1868-0.01450.0340.02550.179-0.004-0.00410.1843-0.00180.163115.08746.132823.1365
31.3373-1.41090.16622.7942-0.92071.86440.07330.10030.3575-0.5209-0.094-0.3376-0.17770.05680.00820.18440.00190.03310.1790.04490.22521.164823.844312.1055
43.59541.676-0.18666.51471.86337.66060.01760.15350.645-0.01650.021-0.3913-0.54490.25910.01450.1920.02860.01150.15650.05720.3979-4.063737.897317.2875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 56 )A-1 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 148 )A57 - 148
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 182 )A149 - 182
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 208 )A183 - 208

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